9VHD | pdb_00009vhd

cryo-EM structure of a chimeric EfpA dimer

PDB DOI: https://doi.org/10.2210/pdb9VHD/pdb
EM Map EMD-65063: EMDB EMDataResource

Classification: PROTEIN BINDING
Organism(s): Mycolicibacterium smegmatis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-06-16 Released: 2026-06-24
Deposition Author(s): Li, D., Sun, J.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.26 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9VHD

This is version 1.0 of the entry. See complete history.

Literature

cryo-EM structure of a chimeric EfpA dimer

Li, D., Sun, J.

To be published.

Macromolecule Content

Total Structure Weight: 106.92 kDa
Atom Count: 6,878
Modeled Residue Count: 944
Deposited Residue Count: 1,032
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative MFS-type transporter EfpA	A [auth B], B [auth A]	516	Mycolicibacterium smegmatis	Mutation(s): 0 Gene Names: efpA_1, BIN_B_04248
UniProt
Find proteins for A0A653FLF0 (Mycolicibacterium smegmatis) Explore A0A653FLF0 Go to UniProtKB: A0A653FLF0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A653FLF0
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.26 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.19.2_4158
RECONSTRUCTION	cryoSPARC

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-06-24

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2026-06-24
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.